During the Hundred Years' War Souillac was twice occupied by the English and the monastery suffered considerable damage.

In 1508, a period of prosperity for Souillac, the church was   officially designated as an abbey. Situated to the south of the Limousin and east of the Perigord, the town of Souillac is one of the most ancient in the Haut Quercy. Souillac, Soliacum in Latin, has changed its name down the ages. First, it was Solhac from the twelfth to the fifteenth century, then Soilhac or Soulhiac in the sixteenth and seventeenth centuries, and finally became Souillac in the eighteenth century.

Traces of prehistoric man have been discovered on the banks of the Borreze , the river which runs through Souillac and then flows into the Dordogne. Flintstone axes from the Neolithic period and other objects from 400-500 B.C., together with remains from the Iron Age, have been found during excavations.

The first texts mentioning Souillac date from the tenth century, but legend has it that Saint Eligius, minister to King Dagobert, founded a Benedictine monastery there in 655 A.D.
Souillac's growth is founded on the growth of the abbey. Here are some details.

In 909 Saint Gerald, Count of Aurillac, left half his property to the monks of Souillac, who remained dependant on the Bishopric of Aurillac until 1473. The monks drained the marshes and canalized the Borreze and built a church consecrated to the Virgin Mary.

The present abbey church of Saint Mary, Souillac's most beautiful building, was built in the twelfth century. But, in 1562 the town was sacked by the Huguenots and in 1573, the Viscount of Gourdon destroyed the parish church and burned the abbey, which was raised again from its ruins in the following century.
After the French Revolution in 1789 the monastery was dissolved and the abbey became Souillac's parish church. Repairs and renovations were carried out in 1841 and the church was classified as a national monument. Most of the interior wall decorations on plaster which dated from this time were removed again in the early 1970s.

In 1932 the original pitched and tiled roof was removed and the three domes, which became visible, were recovered in limestone.

Framing the inside of the door of the church are fragments of sculpture taken from an outer portal which was severely damaged during the wars of religion. The twelfth-century bas-relief of the prophet Isaiah is a fragment of what once must have been a masterpiece by one of the greatest sculptors of the Romanesque era. The other pieces, though interesting, are stiff in comparison.

In 1950 monolithic sarcophagi, tombs and other Carlovingian vestiges were found during excavation work.